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Questions tagged [rdkit]

RDKit is a popular open-source library for chemoinformatics and machine learning applied to chemoinformatics.

RDKit is a popular open-source library for chemoinformatics and machine learning applied to chemoinformatics.

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How to deal with the peptide sequences that have atypical amino acids in the seuqnces?

I am not a bioinformatician and my question may sound basic. I have some issues with RDKit The issue: there are some sequences that have X in the antimicrobial peptide sequence. Seems that RDKit cannot process these cases. For example the following…
S.EB
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RDKit: Atom Indices to *.mol file

Question: How to convert atom indices into mol file? Goal: Convert shortest path between atoms into mol file. I have an initial mol file and am analyzing it using RDKit. I am getting the shortest path between two atoms using their indices. Example…
meadeytabeedy
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AttributeError: type object 'Molecule' has no attribute 'dummy_atom'

I am trying to reproduce the example from this documentation of chemicalX here. But I am receiving this error AttributeError: type object 'Molecule' has no attribute 'dummy_atom'. I have tried to look into the documentation and found out there is no…
harsh
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Implement RDKit and Postgres in Django

I started to use rdkit and try to implement in Django with postgres. So I installed rdkit in my django virtualenv with pip install rdkit-pypi and also installed django-rdkit(https://github.com/rdkit/django-rdkit). This command: python3 -c "from…
Joanna
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RDKIT export dataframe to .mol or .sdf file

I need to convert a bunch of Smiles into mold2 using this GUI tools (https://www.fda.gov/files/science%20&%20research/published/Mold2-Tutorial.pdf) How do I convert pandas data frame into either .mol or .sdf file?
Petr
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Can someone tell why Chem.MolFromSmiles is not converting list of SMILES into mol objects in RDKit?

I have a list of 298 SMILES and I want to turn those 298 into mol objects however rdkit is giving me the above error. TypeError: No registered converter was able to produce a C++ rvalue of type std::basic_string
Cris Silva
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Is there a way to use RDKit without Anaconda or Conda?

RDKit is a Python library for chemistry. I don't want to use an Anaconda distribution, and I am not sure (from the documentation: https://www.rdkit.org/docs/Install.html ) if there is a way to use the package without it. Can someone give me some…
girlsway.app
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How to create a boost property map between rdkit molecular bond graph edges and BGL biconnected component identifiers?

The rdkit library provides a molecule class ROMol that provides a member function getTopology that returns a BGL graph of type adjacency_list. I understand that the rdkit type Bond defines the edge properties…
Quappas
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ArgumentError: Python argument types in rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(NoneType, int) did not match C++ signature

So I'm working with RDKit and Python to convert SMILES strings to ECFP4 fingerprints, and my code is as shown below. I got an error, but I have also checked with this question over here but I seem to have the correct code? But why am I still getting…
azwaar
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RDKit crashing Notebook Kernel on import

I installed RDKit via pip like this. pip install rdkit-pypi and whenever I import any rdkit module: from rdkit.Chem.Draw import IPythonConsole I get this in VSCode. Error The kernel '.pyvenv (Python 3.9.7)' died. View Jupyter…
Shahzad Akram
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C++ error message when using python with rdkit

I am using rdkit to use tanimoto similarity to compare molecular fingerprints. However, when I do so, it gives me an error regarding C++. I'm not sure whats incorrect in my code. I provided a code a used earlier that ran sucessfully to help to…
user14737614
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Changing the font of atom label in rdkit

I'm trying to change the font type of the atom labels in RDKIT. The default font type is 'sans'. I ran this code on colab: from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import Draw smiles = 'C1=CC=C(C=C1)I' mol…
YonHar
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RDKit hook for Pyinstaller to create .exe file

I'm trying to export a Python file as a .exe file with Pyinstaller. My Python program uses the RDKit package, which is not supported by Pyinstaller by default. I tried to set the flag --hidden-import='rdkit' and I also placed a hook file in the…
Gianluca Armeli
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Why i can't get 3D mol structure in RDkit?

I have edited the molecule as I wanted. Now I have to export it. But mol blocks always look 2D. So my molecules become 2D. I want to get a 3D structure. Does anyone know the solution? (look at the image for the screenshot)
Aykut Elmas
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Compound classification using RDkit

How to classify compound computationally using RDkit or other libraries? For example, how to tell if a compound is a halide, Amine or Alcohol? Does RDkit have build in functions for this kind of task?
sudododo
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